The announcement on Friday that Katie Holmes had filed for divorce from Tom Cruise didn’t come as a surprise to many who’ve questioned the relationship from its early Oprah-couch-bouncing days. The revelation that she’s seeking sole legal custody and primary residential custody of their 6-year-old daughter Suri? Now that’s news.

Unless a parent feels that a child is in danger, sole custody in divorce proceedings can be a pretty steep uphill battle. Holmes’ filing means she wants to take control of her daughter’s health, education and religion, and that she believes she and Cruise won’t see eye to eye on these crucial decisions. If the chatter is to believed, Cruise’s devotion to Scientology is driving her concerns.

Celebrity websites, including TMZ, are reporting that Holmes was worried that Cruise would spirit their daughter away to join the Sea Organization, a.k.a. Sea Org — a fraternal order of Scientology’s crème de la crème, its most ardent acolytes. Other websites, like PerezHilton.com, said Cruise wanted to board Suri on Freewinds, the Scientology cruise ship that once hosted his birthday bash. The speculation reached fever pitch here:

It’s not our place to judge how someone wants to raise their child … but if you ask us — sending a kindergartner to a military-style boarding school on the high seas, to be raised by people who sign a contract to work for the ship for a BILLION years is borderline abusive.

Alas, the real story is likely not quite as juicy. Freewinds is not a floating boarding school; it’s a pricey destination for Scientologists who want to learn more about their religion. Children are said to be rarely allowed on board.

As for Sea Org, although it’s true that its devotees make a 1 billion-year pledge as a sign of “their eternal commitment to the religion,” children under 14 are not accepted. The pledge is symbolic, but joining Sea Org is still a huge step, perhaps akin to entering a monastery. In the ultimate proof of devotion to the church, active Sea Org members are not allowed to have children.

For other Scientologists who do have kids, however, their religion has some pretty specific beliefs about how to raise them. On the website Scientology Parent, there are plenty of articles on child rearing; some don’t appear to differ much from those on any number of mommy blogs — posts on au pairs and raising physically fit kids, for example. But scroll down — you’ll find a recipe for homemade infant barley formula — and it’s clear this isn’t for your ordinary frazzled mom or pop wondering how to get their kid to stop grumbling and do his chores.

In one post, “Why Parent-Child Relationships Go Sour,” blogger Tad Reeves talks about the principle of “exchange” — in which children give back to their family — and quotes Scientology founder L. Ron Hubbard: “Parental-child relationships are sour, really, only for one good reason. And that is because the child cannot contribute equally to the parent contributions. This demonstrates the child to be much less powerful than the parents; it makes him — puts him in a bad way.”

In another post, Reeves rails against the prescription of psychiatric drugs to children, warning that “if someone ever, ever attempts to label the normal behavior of my children and push them onto mind-destroying drugs — Lord help them.” His comments echo the against-the-grain statements that Cruise made in 2005 about actress Brooke Shields’ postpartum depression, which she treated with Paxil. In a contentious interview, Cruise told Today show host Matt Lauer that “there’s no such thing as a chemical imbalance” and that antidepressants only “mask the problem.” Shields, Cruise went on, should have used vitamins and exercise to heal herself:

“Here’s the problem. You don’t know the history of psychiatry,” he told Lauer. “I do … The thing that I’m saying about Brooke is that there’s misinformation, O.K. And she doesn’t understand the history of psychiatry. She doesn’t understand in the same way that you don’t understand it, Matt.”

It’s possible that Holmes, who was raised Catholic, first started getting cold feet as Suri’s due date approached. Cruise reportedly wanted Holmes to have a “silent birth” — a Scientologist’s ideal way to deliver a child. According to Scientology Newsroom, the church’s official media resource center, founder Hubbard stated that “particularly during birth, absolute silence must be maintained” by everyone around the mother (the no-words rule doesn’t apply to the mother herself; the site notes that “it is doubtful that any woman could give birth without making any noise at all.” For sure, there’s little to argue with in that statement). Scientology Newsroom explains:

“L. Ron Hubbard discovered the hidden source of nightmares, unreasonable fears, upsets, insecurity and psychosomatic illness — the reactive mind. This part of the mind records all perceptions during times of pain and unconsciousness — which childbirth is for both mother and child. And words, in particular, spoken during these moments, can have an adverse effect on one later in life.”

Practices like silent birth, along with adherence to other strict moral and practical guidelines, have prompted critics to label Scientology a cult. “Scientology is a potentially unsafe, if not dangerous, organization,” Rick Ross, a New Jersey–based expert on cults and controversial movements who has served as an expert witness in court cases, told Reuters. “I’ve received complaint after complaint over the years from former members.”

Children raised according to the tenets of Scientology are given a tremendous amount of responsibility and are allowed to make significant decisions; some are even able to decide when to start formal schooling. If finances permit, they attend one of about 50 Scientology schools in the U.S. or receive religious tutoring that supplements public-school education. In theory, parents help construct a self-contained world for children, so all their teachers — including dance instructors and soccer coaches — ideally practice Scientology.

Author Janet Reitman has more insight than most into the beliefs of Scientologists. She wrote Inside Scientology, which was published last July and based in part on her 2006 article in Rolling Stone that focused on the experience of young Scientologists. In this excerpt from the article, she talks about Natalie Walet, whom Reitman met when Walet was a 17-year-old practitioner:

Natalie’s everyday reality is one of total immersion in all things Hubbard. Scientology kids are raised in a very different manner than mainstream kids. Most of them, like Natalie, have been educated by special tutors, and enrolled, as Natalie was when she was younger, in private schools run by Scientologists that use a Hubbard-approved study technique. Most kids are also put “on course” — enrolled in classes at the church that teach both children and adults self-control, focus and communication skills. Natalie was put on course, upon her own insistence, when she was 7 or 8 years old. Between school and church, life was “kind of a bubble,” she says.

Tensions in the Cruise-Holmes household had reportedly been simmering for a while over how central a role Scientology should play in Suri’s life. Apparently, Holmes is not a big fan of bubbles.